PXD039165-1

PXD039165 is an original dataset announced via ProteomeXchange.

Title	A Dataset for Developing Proteomic Tools in Pathogen Detection via Differential Cell Lysis from Whole Blood Samples
Description	This data descriptor introduces a curated dataset generated through a methodology that merges differential cell lysis, paired with swift extraction/digestion processes and mass spectrometry-based proteomics, aimed at the specific detection and identification of pathogens such as Staphylococcus aureus, Pseudomonas aeruginosa, and Candida albicans directly from whole-blood samples. Our protocol offers a rapid and direct diagnostic alternative, circumventing the traditional culture processes and thus facilitating the timely management of diseases like sepsis. We demonstrate the utility of this dataset by proposing a biomarker panel, derived from the proteomic profiles of the aforementioned pathogens, and applying our differential cell lysis protocol to blood samples from 8 sepsis patients. We achieved a sensitivity of 87.5% using parallel reaction monitoring (PRM), thereby providing diagnostics within a seven-hour timeframe without the need for microbial enrichment culture. Moreover, this dataset demonstrates high reproducibility and minimal outliers, solidifying its role as a reference for benchmarking and development of bioinformatic tools for peptide panel in identification for microbial detection, antimicrobial resistance, and epidemiological studies.
HostingRepository	PRIDE
AnnounceDate	2024-08-08
AnnouncementXML	Submission_2024-08-08_02:41:26.607.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Marlon D M Santos
SpeciesList	scientific name: Candida albicans (Yeast); NCBI TaxID: 5476; scientific name: Pseudomonas aeruginosa PABL056; NCBI TaxID: 1214916; scientific name: Staphylococcus aureus; NCBI TaxID: 1280;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-01-02 18:59:56	ID requested
⏵ 1	2024-08-08 02:41:27	announced

Dataset with its publication pending

submitter keyword: bloodstream infection, fungi identification, PRM, mass spectrometry, bacteria identification,Sepsis, rapid diagnosis, whole blood, LC-MS/MS

Jéssica de
contact affiliation	Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Fiocruz Parana, Parana, Brazil
contact email	jessica_oliveiraveloso@hotmail.com
lab head
Marlon D M Santos
contact affiliation	Computational Mass Spectrometry & Proteomics Group - Fiocruz
contact email	marlondms@gmail.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/08/PXD039165

PRIDE project URI

• PRIDE
  1. PXD039165
     1. Label: PRIDE project
     2. Name: A Dataset for Developing Proteomic Tools in Pathogen Detection via Differential Cell Lysis from Whole Blood Samples